Sample summary
| Barcode | Alias | Read count | Median read length | Contig count | MLST | Species call (ANI | Fraction query) |
|---|---|---|---|---|---|---|
| barcode01 | test1 | 22031 | 5908.0 | 2 | mycobacteria_2 | Mycobacterium tuberculosis ( 0.999 | 0.970) |
| barcode02 | test2 | 7076 | 3328.0 | 331 | senterica_achtman_2 | Salmonella enterica ( 0.987 | 0.523) |
ANI: Average Nucleotide Identity
Fraction query: Fraction of query genome matched to reference
Read summary
Reads were filtered and summary statistics were generated using
fastcat.
Use the dropdown menu to view different samples.
Assembly summary statistics
Assembly QC statistics reported by
Flye following de novo assembly.
You can use the dropdown menu to view different samples.
| Contig | Length (bp) | Coverage | Circular | Repeat | Multiplicity |
|---|---|---|---|---|---|
| contig_1 | 4415551 | 34.0 | N | N | 1 |
| contig_2 | 113211 | 205.0 | N | Y | 5 |
| Contig | Length (bp) | Coverage | Circular | Repeat | Multiplicity |
|---|---|---|---|---|---|
| contig_323 | 59596 | 6.0 | N | N | 1 |
| contig_277 | 42175 | 5.0 | N | N | 1 |
| contig_300 | 38841 | 4.0 | N | N | 1 |
| contig_316 | 35380 | 5.0 | N | N | 1 |
| contig_287 | 34854 | 5.0 | N | N | 1 |
| contig_315 | 34603 | 4.0 | N | N | 1 |
| contig_269 | 34317 | 5.0 | N | N | 1 |
| contig_297 | 33882 | 5.0 | N | N | 1 |
| contig_275 | 32126 | 4.0 | N | N | 1 |
| contig_285 | 31539 | 4.0 | N | N | 1 |
| contig_296 | 31004 | 5.0 | N | N | 1 |
| contig_1 | 29762 | 5.0 | N | N | 1 |
| contig_113 | 29247 | 7.0 | N | N | 2 |
| contig_319 | 28236 | 7.0 | N | N | 2 |
| contig_281 | 27573 | 6.0 | N | N | 1 |
| contig_25 | 26878 | 4.0 | N | N | 1 |
| contig_317 | 26274 | 6.0 | N | N | 1 |
| contig_302 | 25673 | 4.0 | N | N | 1 |
| contig_119 | 25580 | 6.0 | N | N | 1 |
| contig_331 | 25444 | 6.0 | N | N | 1 |
| contig_51 | 25439 | 7.0 | N | N | 1 |
| contig_311 | 25303 | 8.0 | N | N | 2 |
| contig_223 | 24704 | 5.0 | N | N | 1 |
| contig_318 | 24591 | 5.0 | N | N | 1 |
| contig_330 | 24534 | 5.0 | N | N | 1 |
| contig_262 | 23802 | 4.0 | N | N | 1 |
| contig_288 | 23637 | 6.0 | N | N | 1 |
| contig_270 | 23576 | 5.0 | N | N | 1 |
| contig_276 | 23568 | 6.0 | N | N | 1 |
| contig_75 | 23153 | 4.0 | N | N | 1 |
| contig_320 | 22817 | 5.0 | N | N | 1 |
| contig_21 | 22762 | 5.0 | N | N | 1 |
| contig_52 | 22592 | 5.0 | N | N | 1 |
| contig_193 | 22505 | 6.0 | N | N | 1 |
| contig_56 | 22289 | 4.0 | N | N | 1 |
| contig_263 | 22205 | 4.0 | N | N | 1 |
| contig_293 | 22192 | 6.0 | N | N | 1 |
| contig_133 | 22042 | 8.0 | N | N | 2 |
| contig_294 | 21953 | 3.0 | N | N | 1 |
| contig_132 | 21643 | 6.0 | N | N | 1 |
| contig_284 | 21360 | 4.0 | N | N | 1 |
| contig_271 | 21338 | 4.0 | N | N | 1 |
| contig_44 | 21017 | 4.0 | N | N | 1 |
| contig_295 | 20708 | 6.0 | N | N | 1 |
| contig_145 | 20451 | 3.0 | N | N | 1 |
| contig_91 | 20441 | 5.0 | N | N | 1 |
| contig_22 | 20381 | 3.0 | N | N | 1 |
| contig_153 | 20201 | 5.0 | N | N | 1 |
| contig_321 | 20123 | 6.0 | N | N | 1 |
| contig_282 | 19855 | 6.0 | N | N | 1 |
| contig_16 | 19789 | 9.0 | N | Y | 2 |
| contig_305 | 19577 | 5.0 | N | N | 1 |
| contig_15 | 19149 | 8.0 | N | N | 2 |
| contig_47 | 19125 | 5.0 | N | N | 1 |
| contig_134 | 18934 | 5.0 | N | N | 1 |
| contig_301 | 18578 | 3.0 | N | N | 1 |
| contig_197 | 18319 | 5.0 | N | N | 1 |
| contig_100 | 18287 | 4.0 | N | N | 1 |
| contig_252 | 18255 | 5.0 | N | N | 1 |
| contig_265 | 18224 | 5.0 | N | N | 1 |
| contig_298 | 18162 | 4.0 | N | N | 1 |
| contig_310 | 18154 | 6.0 | N | N | 1 |
| contig_226 | 18117 | 7.0 | N | N | 2 |
| contig_258 | 18029 | 5.0 | N | N | 1 |
| contig_77 | 17600 | 7.0 | N | N | 2 |
| contig_104 | 17430 | 7.0 | N | N | 2 |
| contig_309 | 17316 | 6.0 | N | N | 1 |
| contig_306 | 16929 | 5.0 | N | N | 1 |
| contig_57 | 16733 | 8.0 | N | N | 2 |
| contig_304 | 16709 | 5.0 | N | N | 1 |
| contig_278 | 16642 | 5.0 | N | N | 1 |
| contig_5 | 16549 | 4.0 | N | N | 1 |
| contig_103 | 16400 | 4.0 | N | N | 1 |
| contig_146 | 16321 | 4.0 | N | N | 1 |
| contig_244 | 16113 | 4.0 | N | N | 1 |
| contig_240 | 15921 | 5.0 | N | N | 1 |
| contig_128 | 15833 | 3.0 | N | N | 1 |
| contig_115 | 15785 | 4.0 | N | N | 1 |
| contig_70 | 15748 | 6.0 | N | N | 1 |
| contig_121 | 15504 | 3.0 | N | N | 1 |
| contig_261 | 15468 | 5.0 | N | N | 1 |
| contig_303 | 15315 | 5.0 | N | N | 1 |
| contig_208 | 15133 | 5.0 | N | N | 1 |
| contig_328 | 15014 | 4.0 | N | N | 1 |
| contig_246 | 14971 | 5.0 | N | N | 1 |
| contig_299 | 14936 | 6.0 | N | N | 1 |
| contig_255 | 14777 | 6.0 | N | N | 1 |
| contig_72 | 14707 | 5.0 | N | N | 1 |
| contig_247 | 14662 | 7.0 | N | N | 2 |
| contig_114 | 14635 | 6.0 | N | N | 1 |
| contig_283 | 14622 | 7.0 | N | N | 1 |
| contig_312 | 14290 | 5.0 | N | N | 1 |
| contig_13 | 14282 | 8.0 | N | N | 2 |
| contig_170 | 14191 | 3.0 | N | N | 1 |
| contig_118 | 13733 | 7.0 | N | N | 1 |
| contig_157 | 13727 | 6.0 | N | N | 1 |
| contig_34 | 13654 | 5.0 | N | N | 1 |
| contig_40 | 13617 | 5.0 | N | N | 1 |
| contig_207 | 13585 | 5.0 | N | N | 1 |
| contig_324 | 13357 | 5.0 | N | N | 1 |
| contig_313 | 13353 | 6.0 | N | N | 1 |
| contig_67 | 13204 | 5.0 | N | N | 1 |
| contig_46 | 13198 | 5.0 | N | N | 1 |
| contig_291 | 13059 | 5.0 | N | N | 1 |
| contig_192 | 13005 | 11.0 | N | Y | 3 |
| contig_166 | 12982 | 6.0 | N | N | 1 |
| contig_307 | 12974 | 10.0 | N | Y | 2 |
| contig_50 | 12740 | 5.0 | N | N | 1 |
| contig_36 | 12651 | 5.0 | N | N | 1 |
| contig_116 | 12613 | 6.0 | N | N | 1 |
| contig_14 | 12538 | 3.0 | N | N | 1 |
| contig_164 | 12358 | 4.0 | N | N | 1 |
| contig_280 | 12348 | 5.0 | N | N | 1 |
| contig_183 | 12345 | 7.0 | N | N | 2 |
| contig_88 | 12217 | 4.0 | N | N | 1 |
| contig_242 | 12195 | 5.0 | N | N | 1 |
| contig_8 | 12192 | 5.0 | N | N | 1 |
| contig_76 | 12161 | 5.0 | N | N | 1 |
| contig_259 | 12139 | 8.0 | N | N | 2 |
| contig_7 | 12138 | 4.0 | N | N | 1 |
| contig_272 | 12105 | 5.0 | N | N | 1 |
| contig_292 | 12031 | 4.0 | N | N | 1 |
| contig_102 | 12023 | 5.0 | N | N | 1 |
| contig_20 | 12014 | 6.0 | N | N | 1 |
| contig_181 | 11923 | 4.0 | N | N | 1 |
| contig_3 | 11818 | 3.0 | N | N | 1 |
| contig_159 | 11761 | 6.0 | N | N | 1 |
| contig_117 | 11742 | 6.0 | N | N | 1 |
| contig_122 | 11718 | 4.0 | N | N | 1 |
| contig_329 | 11503 | 4.0 | N | N | 1 |
| contig_160 | 11462 | 5.0 | N | N | 1 |
| contig_93 | 11459 | 5.0 | N | N | 1 |
| contig_9 | 11420 | 6.0 | N | N | 1 |
| contig_73 | 11412 | 5.0 | N | N | 1 |
| contig_154 | 11371 | 6.0 | N | N | 1 |
| contig_78 | 11326 | 7.0 | N | N | 1 |
| contig_82 | 11297 | 8.0 | N | N | 2 |
| contig_325 | 11131 | 5.0 | N | N | 1 |
| contig_314 | 11048 | 4.0 | N | N | 1 |
| contig_327 | 11015 | 5.0 | N | N | 1 |
| contig_221 | 10859 | 7.0 | N | N | 2 |
| contig_23 | 10656 | 5.0 | N | N | 1 |
| contig_2 | 10607 | 6.0 | N | N | 1 |
| contig_268 | 10533 | 5.0 | N | N | 1 |
| contig_289 | 10490 | 6.0 | N | N | 1 |
| contig_147 | 10480 | 4.0 | N | N | 1 |
| contig_161 | 10445 | 7.0 | N | N | 2 |
| contig_19 | 10294 | 4.0 | N | N | 1 |
| contig_182 | 10264 | 5.0 | N | N | 1 |
| contig_203 | 10240 | 5.0 | N | N | 1 |
| contig_31 | 10152 | 3.0 | N | N | 1 |
| contig_143 | 10088 | 3.0 | N | N | 1 |
| contig_127 | 10078 | 6.0 | N | N | 1 |
| contig_273 | 10062 | 6.0 | N | N | 1 |
| contig_41 | 9996 | 4.0 | N | N | 1 |
| contig_124 | 9984 | 5.0 | N | N | 1 |
| contig_308 | 9910 | 3.0 | N | N | 1 |
| contig_112 | 9862 | 7.0 | N | N | 1 |
| contig_326 | 9854 | 5.0 | N | N | 1 |
| contig_257 | 9839 | 6.0 | N | N | 1 |
| contig_266 | 9810 | 5.0 | N | N | 1 |
| contig_322 | 9773 | 7.0 | N | N | 1 |
| contig_49 | 9755 | 5.0 | N | N | 1 |
| contig_279 | 9611 | 4.0 | N | N | 1 |
| contig_81 | 9569 | 5.0 | N | N | 1 |
| contig_108 | 9459 | 4.0 | N | N | 1 |
| contig_169 | 9435 | 9.0 | N | Y | 2 |
| contig_138 | 9389 | 5.0 | N | N | 1 |
| contig_59 | 9351 | 4.0 | N | N | 1 |
| contig_267 | 9305 | 8.0 | N | N | 2 |
| contig_66 | 9234 | 5.0 | N | N | 1 |
| contig_250 | 9198 | 5.0 | N | N | 1 |
| contig_83 | 9189 | 6.0 | N | N | 1 |
| contig_253 | 9112 | 6.0 | N | N | 1 |
| contig_165 | 8880 | 3.0 | N | N | 1 |
| contig_97 | 8851 | 7.0 | N | N | 2 |
| contig_126 | 8793 | 6.0 | N | N | 1 |
| contig_71 | 8731 | 7.0 | N | N | 2 |
| contig_256 | 8703 | 5.0 | N | N | 1 |
| contig_26 | 8678 | 7.0 | N | N | 1 |
| contig_110 | 8633 | 3.0 | N | N | 1 |
| contig_142 | 8629 | 5.0 | N | N | 1 |
| contig_251 | 8466 | 4.0 | N | N | 1 |
| contig_64 | 8439 | 5.0 | N | N | 1 |
| contig_11 | 8361 | 4.0 | N | N | 1 |
| contig_176 | 8357 | 7.0 | N | N | 2 |
| contig_125 | 8281 | 6.0 | N | N | 1 |
| contig_129 | 8255 | 6.0 | N | N | 1 |
| contig_99 | 8244 | 4.0 | N | N | 1 |
| contig_173 | 8231 | 3.0 | N | N | 1 |
| contig_198 | 8204 | 4.0 | N | N | 1 |
| contig_39 | 8191 | 5.0 | N | N | 1 |
| contig_139 | 8145 | 5.0 | N | N | 1 |
| contig_196 | 8010 | 4.0 | N | N | 1 |
| contig_101 | 7993 | 7.0 | N | N | 2 |
| contig_152 | 7990 | 6.0 | N | N | 1 |
| contig_35 | 7958 | 4.0 | N | N | 1 |
| contig_227 | 7921 | 3.0 | N | N | 1 |
| contig_94 | 7884 | 4.0 | N | N | 1 |
| contig_4 | 7683 | 8.0 | N | N | 2 |
| contig_37 | 7665 | 4.0 | N | N | 1 |
| contig_74 | 7607 | 6.0 | N | N | 1 |
| contig_156 | 7588 | 7.0 | N | N | 1 |
| contig_195 | 7568 | 5.0 | N | N | 1 |
| contig_224 | 7563 | 4.0 | N | N | 1 |
| contig_155 | 7545 | 3.0 | N | N | 1 |
| contig_168 | 7535 | 4.0 | N | N | 1 |
| contig_10 | 7448 | 4.0 | N | N | 1 |
| contig_18 | 7356 | 8.0 | N | N | 2 |
| contig_130 | 7348 | 3.0 | N | N | 1 |
| contig_131 | 7297 | 4.0 | N | N | 1 |
| contig_43 | 7240 | 4.0 | N | N | 1 |
| contig_191 | 7229 | 4.0 | N | N | 1 |
| contig_6 | 7221 | 4.0 | N | N | 1 |
| contig_85 | 7207 | 4.0 | N | N | 1 |
| contig_123 | 7152 | 6.0 | N | N | 1 |
| contig_200 | 7076 | 6.0 | N | N | 1 |
| contig_243 | 7055 | 3.0 | N | N | 1 |
| contig_248 | 7055 | 9.0 | N | N | 2 |
| contig_120 | 7043 | 5.0 | N | N | 1 |
| contig_69 | 7034 | 8.0 | N | N | 2 |
| contig_201 | 6999 | 5.0 | N | N | 1 |
| contig_205 | 6972 | 5.0 | N | N | 1 |
| contig_254 | 6902 | 5.0 | N | N | 1 |
| contig_33 | 6835 | 6.0 | N | N | 1 |
| contig_92 | 6748 | 5.0 | N | N | 1 |
| contig_45 | 6737 | 5.0 | N | N | 1 |
| contig_55 | 6669 | 5.0 | N | N | 1 |
| contig_216 | 6646 | 3.0 | N | N | 1 |
| contig_239 | 6535 | 6.0 | N | N | 1 |
| contig_89 | 6509 | 7.0 | N | N | 2 |
| contig_109 | 6496 | 3.0 | N | N | 1 |
| contig_194 | 6469 | 5.0 | N | N | 1 |
| contig_105 | 6392 | 3.0 | N | N | 1 |
| contig_61 | 6370 | 6.0 | N | N | 1 |
| contig_228 | 6332 | 5.0 | N | N | 1 |
| contig_190 | 6315 | 6.0 | N | N | 1 |
| contig_187 | 6264 | 6.0 | N | N | 1 |
| contig_87 | 6264 | 6.0 | N | N | 1 |
| contig_137 | 6244 | 5.0 | N | N | 1 |
| contig_260 | 6237 | 5.0 | N | N | 1 |
| contig_38 | 6224 | 4.0 | N | N | 1 |
| contig_79 | 6214 | 6.0 | N | N | 1 |
| contig_213 | 6200 | 4.0 | N | N | 1 |
| contig_172 | 6196 | 3.0 | N | N | 1 |
| contig_211 | 6156 | 4.0 | N | N | 1 |
| contig_140 | 6046 | 4.0 | N | N | 1 |
| contig_175 | 6043 | 3.0 | N | N | 1 |
| contig_177 | 6002 | 6.0 | N | N | 1 |
| contig_144 | 6001 | 3.0 | N | N | 1 |
| contig_188 | 5971 | 4.0 | N | N | 1 |
| contig_98 | 5907 | 4.0 | N | N | 1 |
| contig_204 | 5861 | 4.0 | N | N | 1 |
| contig_90 | 5792 | 7.0 | N | N | 2 |
| contig_264 | 5790 | 5.0 | N | N | 1 |
| contig_32 | 5767 | 5.0 | N | N | 1 |
| contig_158 | 5759 | 4.0 | N | N | 1 |
| contig_17 | 5748 | 7.0 | N | N | 1 |
| contig_290 | 5715 | 4.0 | N | N | 1 |
| contig_62 | 5664 | 6.0 | N | N | 1 |
| contig_80 | 5647 | 7.0 | N | N | 2 |
| contig_219 | 5636 | 6.0 | N | N | 1 |
| contig_274 | 5597 | 39.0 | N | Y | 10 |
| contig_241 | 5461 | 8.0 | N | N | 2 |
| contig_231 | 5441 | 4.0 | N | N | 1 |
| contig_149 | 5429 | 4.0 | N | N | 1 |
| contig_286 | 5344 | 4.0 | N | N | 1 |
| contig_24 | 5245 | 5.0 | N | N | 1 |
| contig_58 | 5200 | 4.0 | N | N | 1 |
| contig_225 | 5142 | 5.0 | N | N | 1 |
| contig_234 | 5098 | 3.0 | N | N | 1 |
| contig_96 | 5057 | 5.0 | N | N | 1 |
| contig_202 | 5047 | 4.0 | N | N | 1 |
| contig_48 | 5038 | 5.0 | N | N | 1 |
| contig_30 | 5022 | 4.0 | N | N | 1 |
| contig_65 | 4996 | 3.0 | N | N | 1 |
| contig_60 | 4989 | 7.0 | N | N | 1 |
| contig_210 | 4984 | 3.0 | N | N | 1 |
| contig_54 | 4956 | 6.0 | N | N | 1 |
| contig_151 | 4893 | 5.0 | N | N | 1 |
| contig_29 | 4863 | 4.0 | N | N | 1 |
| contig_107 | 4824 | 3.0 | N | N | 1 |
| contig_162 | 4796 | 6.0 | N | N | 1 |
| contig_86 | 4700 | 4.0 | N | N | 1 |
| contig_232 | 4664 | 3.0 | N | N | 1 |
| contig_220 | 4629 | 5.0 | N | N | 1 |
| contig_141 | 4620 | 3.0 | N | N | 1 |
| contig_230 | 4597 | 3.0 | N | N | 1 |
| contig_12 | 4584 | 4.0 | N | N | 1 |
| contig_171 | 4584 | 5.0 | N | N | 1 |
| contig_84 | 4425 | 7.0 | N | N | 1 |
| contig_233 | 4420 | 3.0 | N | N | 1 |
| contig_42 | 4396 | 7.0 | N | N | 1 |
| contig_199 | 4382 | 6.0 | N | N | 1 |
| contig_249 | 4373 | 6.0 | N | N | 1 |
| contig_186 | 4114 | 3.0 | N | N | 1 |
| contig_167 | 4017 | 4.0 | N | N | 1 |
| contig_95 | 3998 | 4.0 | N | N | 1 |
| contig_215 | 3994 | 5.0 | N | N | 1 |
| contig_179 | 3973 | 3.0 | N | N | 1 |
| contig_180 | 3971 | 4.0 | N | N | 1 |
| contig_209 | 3958 | 3.0 | N | N | 1 |
| contig_174 | 3950 | 4.0 | N | N | 1 |
| contig_135 | 3935 | 5.0 | N | N | 1 |
| contig_235 | 3872 | 4.0 | N | N | 1 |
| contig_222 | 3828 | 5.0 | N | N | 1 |
| contig_245 | 3777 | 3.0 | N | N | 1 |
| contig_238 | 3709 | 3.0 | N | N | 1 |
| contig_185 | 3692 | 4.0 | N | N | 1 |
| contig_163 | 3670 | 6.0 | N | N | 1 |
| contig_218 | 3640 | 3.0 | N | N | 1 |
| contig_150 | 3484 | 7.0 | N | N | 2 |
| contig_136 | 3483 | 4.0 | N | N | 1 |
| contig_148 | 3442 | 4.0 | N | N | 1 |
| contig_63 | 3440 | 6.0 | N | N | 1 |
| contig_27 | 3422 | 4.0 | N | N | 1 |
| contig_189 | 3398 | 8.0 | N | N | 1 |
| contig_236 | 3319 | 3.0 | N | N | 1 |
| contig_214 | 3246 | 3.0 | N | N | 1 |
| contig_111 | 3223 | 9.0 | N | Y | 2 |
| contig_53 | 3178 | 4.0 | N | N | 1 |
| contig_206 | 2978 | 6.0 | N | N | 1 |
| contig_184 | 2976 | 5.0 | N | N | 1 |
| contig_229 | 2911 | 3.0 | N | N | 1 |
| contig_217 | 2904 | 3.0 | N | N | 1 |
| contig_237 | 2682 | 3.0 | N | N | 1 |
| contig_106 | 2617 | 7.0 | N | N | 1 |
| contig_212 | 2577 | 7.0 | N | N | 1 |
| contig_28 | 2455 | 4.0 | N | N | 1 |
| contig_178 | 2384 | 6.0 | N | N | 1 |
| contig_68 | 2250 | 3.0 | N | N | 1 |
Plasmid identification
Plasmid identification was performed using
MOB-suite
Use the dropdown menu to view different samples.
Click on each plasmid cluster to view detailed information about the contigs.
MOB-suite identified 3 plasmid contigs out of 331 total contigs in this assembly, representing 1 distinct plasmid.
Predicted mobility: non-mobilizable
Best database match (Mash distance): Salmonella enterica subsp. enterica ( 0.0377)
Predicted host range: genus Salmonella
Observed host range: genus Salmonella
| Contig | Length (bp) | Replicon type | Relaxase type | MPF type | oriT type |
|---|---|---|---|---|---|
| contig_44 | 20998 | - | - | - | - |
| contig_220 | 4627 | - | - | - | - |
| contig_42 | 4391 | - | - | - | - |
Mash distance approaching 0 indicates close identity.
Antimicrobial resistance prediction
The assembly was analysed for presence of antimicrobial resistance genes and mutations using
ResFinder.
You can use the dropdown menu to select different samples.
Resistance to the following antimicrobial and disinfectant classes was found:
Genes analysed for AMR point mutations:
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| formA | Formaldehyde | contig_1 | 498 - 1607 | 100.00% | 100.00% | X73835 | 8891129 | DisinFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| aac(2')-Ic | Dibekacin, Gentamicin, Netilmicin, Tobramycin | contig_1 | 314726 - 315271 | 100.00% | 100.00% | U72714 | unpublished | ResFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| erm(37) | Clindamycin, Lincomycin | contig_1 | 2232096 - 2232635 | 100.00% | 100.00% | AL123456 | 9634230 | ResFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| erm(37) | Erythromycin, Telithromycin | contig_1 | 2232096 - 2232635 | 100.00% | 100.00% | AL123456 | 9634230 | ResFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| qacD | Benzylkonium Chloride, Cetylpyridinium Chloride, Chlorhexidine, Ethidium Bromide | contig_1 | 4411882 - 4413866 | 99.45% | 98.80% | M37888 | 1840534 | DisinFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ▸ embA-promoter (3) | Ethambutol | contig_1 | 4243534 - 4246933 | 99.88% | 100.00% | LR027516.1 | - | PointFinder | ||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||
Resistance to the following antimicrobial and disinfectant classes was found:
Genes analysed for AMR point mutations:
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database |
|---|---|---|---|---|---|---|---|---|
| aac(6')-Iaa | Amikacin, Tobramycin | contig_312 | 4321 - 4758 | 98.63% | 100.00% | NC_003197 | 11677609 | ResFinder |
| Gene | Drug(s) | Contig | Gene position | Identity | Coverage | Accession | PMID | Database | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ▸ pmrA (1) | Colistin | contig_302 | 14831 - 15499 | 99.10% | 100.00% | CP055130.1 | - | PointFinder | ||||||||||||
|
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Multilocus sequence typing
Multilocus sequencing typing was performed using
MLST. Typing scheme information is available at
PubMLST.
You can use the dropdown menu to select different samples.
| Scheme | Sequence Type | S8 | S19 | S12 | L19 | S7 | S14Z | L16 | L35 |
|---|---|---|---|---|---|---|---|---|---|
| mycobacteria_2 | 215 | 18 | 20 | 20 | 19 | 19 | 17 | 22 | 15 |
| Scheme | Sequence Type | AroC | SucA | PurE | DnaN | HisD | HemD | ThrA |
|---|---|---|---|---|---|---|---|---|
| senterica_achtman_2 | - | 114 | - | ~1203 | - | 114 | 8 | 109 |
Salmonella serotyping
Serotyping was performed using
SeqSero2.
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| Predicted serotype | Predicted antigenic profile | O antigen prediction | H1 antigen prediction(fliC) | H2 antigen prediction(fljB) | Note |
|---|---|---|---|---|---|
| Havana | 13:f,g:- | 13 | f,g | - | nan |
Genome coverage
The plot below illustrates depth of coverage. For adequate variant calling, depth should be at least 50X in any region.
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Coverage for up to 20 longest contigs is displayed for each sample.